As an initiative of WCS, MERMAID is an open-source multi-tool coral reef data platform that helps you:

• Collect and manage data in MERMAID Collect;

• Visualize and share data in MERMAID Explore;

• Export, import and analyze data using the MERMAID R package.

Scientists input their observations directly into MERMAID Collect, where data is automatically tagged and sorted, avoiding duplicates, standardizing scientific names and summarizing critical indicators.

We save you time so you can save coral reefs!

MERMAID joins you in the field with its offline capabilities, but it stands apart from Excel or personal database apps like Access because it requires virtually zero post-entry data clean up! 

Users can select reef fish and coral names from a standard list of taxa with only a few keystrokes; MERMAID will autocomplete the rest. Selecting names means saving time typing in species names or cleaning up typos of misspelled species names.

MERMAID also calculates coral reef health metrics such as reef fish biomass and benthic % cover while you type, before you have even finished entering a transect.

When you have finished collecting data, it can be exported to standard Excel datasets and used to create graphs or other reports. You can also analyze your data by accessing it directly from MERMAID in R using our MERMAID R package. Or simply navigate to MERMAID Explore to view your data as coral reef health metrics alongside data from other MERMAID users in a global map.

The MERMAID workflow:

1. Sign up and set up a project

   1. Sign up for an account

   2. Set up a project and add users

   3. Prepare for offline use

2. Collect data

   1. Select a transect type

   2. Enter site information

   3. Enter management regime

   4. Include benthic attributes and fish species

   5. Complete and save the transect

3. Review and submit 

   1. Validate data

   2. Address errors and warnings

   3. Submit data

4. Export and analyze data

   1. Export to XLSX for further analysis

   2. Analyze directly using our MERMAID R package

Questions? You can reach out to us when online via the Contact link at the bottom of the app. An offline (PDF) version of this documentation is available through the "Download" button at the left menu bar.

Try Easy PQT

Photo benthic quadrat data annotated using CoralNet can now be imported to MERMAID in two ways, i.e., the MERMAID R package mermaidr and Easy PQT shiny app. Using the MERMAID R package mermaidr to upload your photo benthic quadrat data to MERMAID requires a good knowledge of R. If you are familiar with R, you can follow the steps in the documentation section Import your spreadsheets, which has all the information you need, including the video tutorial and examples.

Another way to import your photo benthic quadrat data is using the Easy PQT shiny app. Easy PQT supports MERMAID users, especially users unfamiliar with R, who want to import their CoralNet data to MERMAID. It’s straightforward and user-friendly. Similar to using the MERMAID R package mermaidr, your data will appear on your Collecting Page after you import it using Easy PQT. However, you will need to fill in some of the mandatory fields in Collect before validating and submitting your data. See the Easy PQT workflow below:

Only an admin of a project can import data using Easy PQT and make sure that your project is not a test project. A test project will not appear in the Easy PQT list of projects.

Steps to upload your CoralNet exported data using Easy PQT:

• Prepare a project in Collect with sites, management regimes, organizations, and users added, and data sharing policies set up.

• Export your photo benthic quadrat data from CoralNet, including the short codes, ID numbers, and auxiliary fields. MERMAID will use the ID numbers generated from CoralNet to map CoralNet labels to MERMAID benthic attributes, while the short codes will be used to review the mapping result. You will need to set up your auxiliary fields to contain Sites and Management Regimes that correspond to what you have added on MERMAID, as well as Transect numbers. You are also free to rename your auxiliary fields. To export your data with its auxiliary fields, navigate to “Images” in a CoralNet project. Under the “Image Actions”, select “Export Annotations, CSV”, select the label format "Both", and select the optional columns “Image metadata - date and auxiliary fields”, as shown below:

• Open Easy PQT and follow the instructions. Once you open the Easy PQT, it will automatically ask you to authenticate yourself. This way, Easy PQT can provide a list of your projects. Only project(s) that are not a test project will be shown on the list.

• Select the project to which you want to import your data, then upload your CSV data file. You can click the “browse” button to find the data you want to upload or drag and drop directly to the upload field.

• Match your CoralNet auxiliary fields with the MERMAID Site, Management, and Transect number you’ve prepared in Collect. Once you’re done matching those three columns, Easy PQT will automatically validate them to see if they match the options in the MERMAID project you’ve prepared. If it does not match, you will receive information on which fields do not match and what the available options are. A button to Restart Easy PQT will also appear for you to click and restart the process after fixing the issue(s).

• When all your data in the auxiliary fields are validated, Easy PQT will map your CoralNet labels (using the unique ID numbers) to MERMAID attributes. If it’s not available in Easy PQT, then the MERMAID Benthic attribute field will be left blank and colored in red. You need to select the right benthic attributes by clicking on the field directly and start typing or clicking on the arrow on the right to show the dropdown options. Once you’re done filling in the blank fields, click on the “Confirm” button to continue. Easy PQT will reshape your data to match the MERMAID template.

• Review your reshaped data, then click the “Continue with ingestion” button to import your data to MERMAID. If you think the data is incorrect, you can click the “Restart Easy PQT” button to start the process from the beginning or click the “Get help” button to contact us for further assistance. In this section, you can also download the reshaped data in a CSV format.

• Import your reshaped data to MERMAID by clicking the “Continue with ingestion” button on the Easy PQT app. Your imported data will appear on your Collecting Page.

• Head to your Collecting Page in \][;Collect to fill in the rest of the mandatory fields. After uploading your data, there are still some mandatory fields that you need to fill in. Those mandatory fields include depth, transect length surveyed, and quadrat size. East PQT will automatically assign you (a user that uploads the data) as the observer. Change the observer to the right data collector if you are not the one who collects the data. Once you’re done filling those information, you can validate and submit your transects.

Unsubmitted imported transects will appear on the Collecting Page of the users who imported the data using Easy PQT. You can transfer these unsubmitted sample units to another user through the project’s User Page. Only an admin of a project can perform this action.

All access to MERMAID data, including in Collect, Explore and R package mermaidr is done via an Application Programming Interface (API). If you need custom access to data, for example because you are creating a map or writing your own tool, you can use API documentation here as a guide. The documentation includes a getting started page on how to use the Insomnia API client file included with the MERMAID API code repository to access all API endpoints.

MERMAID generates a suggested citation available on the 'Project Info' page in Collect, which is then included in all exported data files and visible in the "Metadata" section of a site view in Explore. This suggested citation can be edited based on your format preferences.

Only an admin of a project can make changes to the suggested citation.

To make changes to the suggested citation, click on the Edit Citation button and start making changes in the Edit Citation field. After you are done making changes, click the Update Citation button to save it.

If you prefer to use the MERMAID's suggested citation after you make changes, you can simply click the Use Default Citation button on the upper right of the Edit Citation field. Don't forget to click the Update Citation button to save changes.